Title page for ETD etd-04072010-012548

The Roles of Transcription Factors in Nucleotide Excision Repair in Yeast

Degree

Doctor of Philosophy (Ph.D.)

Department

Comparative Biomedical Sciences (Veterinary Medical Sciences)

Advisory Committee

Advisor Name

Title

Li, Shisheng

Committee Chair

Barker, Steven A

Committee Member

Cheng, Henrique

Committee Member

Li, Shulin

Committee Member

Ge, Beilei

Dean's Representative

Keywords

transcription factor

Spt4

Tfb5

RNA polymerase II

Spt5

Rpb9

Rad26

nucleotide excision repair

TCR

GGR

yeast

Saccharomyces cerevisiae

Date of Defense

2010-03-30

Availability

unrestricted

Abstract

Nucleotide excision repair (NER) is a conserved DNA repair mechanism capable of removing a variety of helix-distorting lesions, such as UV-induced cyclobutane pyrimidine dimers (CPDs). NER can be grouped into two pathways: global genomic NER (GGR), which refers to repair throughout the genome, and transcription coupled NER (TCR), which refers to a repair mechanism that is dedicated to the transcribed strand (TS) of actively transcribed genes. In yeast S. cerevisiae, Rad7, Rad16, and Elc1 are specifically required for GGR. TCR is believed to be initiated by RNA polymerase II (Pol II) stalled at a lesion in the TS of a gene. Rad26, the yeast homolog of the human CSB protein, and RPB9, a nonessential subunit of Pol II, play important roles in TCR. However, the exact mechanisms of NER in eukaryotic cells are still elusive.

By using yeast S. cerevisiae as a model organism, this dissertation focused on the functional mechanisms of transcription factor Tfb5, transcription elongation factors Spt4 and Spt5, and the putative yeast transcription repair coupling factor (TRCF) Rad26 in NER, especially in TCR pathway. Tfb5, the tenth subunit of the transcription/repair factor TFIIH, is implicated in one group of the human syndrome trichothiodystrophy (TTD). We found that Tfb5 plays different roles in different NER pathways in yeast. Tfb5 is essential for GGR and Rpb9 mediated TCR. However, Tfb5 is partially dispensable for Rad26 mediated TCR, especially in GGR deficient cells. Spt4 and its interacting partner Spt5 cooperatively suppress TCR only in the absence of Rad26, regardless of the presence of Rpb9. The phosphorylation of C-terminal repeat (CTR) domain of Spt5 by the Bur kinase plays an important role in the suppression. Immunoprecipitation results indicate that Rad26 dynamically associates with Pol II and restrains the binding of Spt4/Spt5 to Pol II. ATPase activity of Rad26 is required for facilitating TCR and for restraining the binding of Spt4/Spt5 to Pol II. Finally, we proposed that Rad26 enhances TCR by restraining the binding of suppressors Spt4/Spt5 to Pol II. These findings provide new insights into the functional mechanisms of Tfb5, Spt4/Spt5 and Rad26 in NER, especially in TCR.